Pressure Correction help

[Sacha Mould]

Hi all,

i'm trying to use simple pressure correction on my coarse-grained
simulation but it seems that i'm having some troubles to set it up.
After the first IBI iteration while votca is doing the post-updates
and error appears. This is what is written on the last lines of the
log file:

Energy Average Err.Est. RMSD Tot-Drift
-------------------------------------------------------------------------------
Pressure 168.538 1.5 58.0002 -0.923779
(bar)
New pressure 168.538
an error occurred:
property not found: pressure
an error occurred:
property not found: pressure
Apply simple pressure correction for interaction B-B
Running subscript 'pressure_cor_simple.pl 168.538 B-
B.pressure_correction'(from tags pressure_cor simple)
csg_get_interaction_property: csg_property failed on getting value
inverse.post_update_options.pressure.simple.scale and no default given
###########################################################################################################################################################################
#
#
#
ERROR:
#
# do_external: subscript /home/lusiterrae/votca/share/votca/scripts/
inverse/pressure_cor_simple.pl 168.538 B-B.pressure_correction (from
tags pressure_cor simple) failed #
#
#
###########################################################################################################################################################################


On the non-bonded interaction section of the settings file i'm
assigning:

<post_update>pressure</post_update>
<post_update_options>
<pressure>
<type>simple</type>
<do>0 0 1</do>
<simple>
<scale>0.35586102</scale>
</simple>
</pressure>
</post_update_options>

In addition, i'm assigning <p-target>1</p-target>.

I wonder what could be missing???

Thanks a lot in advance.

Sacha

[Victor Ruehle]

Hey,

hmm, error message seems a bit misleading here. Did you put it in the
sub tag <inverse> in non-bonded? so full path is
cg.non-bonded.inverse.post_update_options.pressure.simple.scale
and
cg.non-bonded.inverse.p_target

be aware the _, not - in p_target

Best,
Victor

2011/11/8 Sacha Mould <sach...@gmail.com>:

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[Sacha Mould]

Hey Victor,

i put the pressure section in the <non-bonded> section of <inverse>
and p_target is well written. I've tried now to run wjk pressure
correction instead... same problem... but the strange thing is that
when i set wjk votca tries to run 'pressure_cor_simple.pl' instead of
'pressure_cor_wjk.pl':

Energy Average Err.Est. RMSD Tot-Drift
-------------------------------------------------------------------------------

Pressure 169.74 0.51 57.1507 1.25074
(bar)
New pressure 169.74

an error occurred:
property not found: pressure
an error occurred:
property not found: pressure
Apply simple pressure correction for interaction B-B

Running subscript 'pressure_cor_simple.pl 169.74 B-

B.pressure_correction'(from tags pressure_cor simple)
csg_get_interaction_property: csg_property failed on getting value
inverse.post_update_options.pressure.simple.scale and no default given
##########################################################################################################################################################################

#
#
#
ERROR:
#
# do_external: subscript /home/lusiterrae/votca/share/votca/scripts/

inverse/pressure_cor_simple.pl 169.74 B-B.pressure_correction (from

tags pressure_cor simple) failed #
#
#
######################################################################################################################

I'm using Votca last release.

Is there any possibility of being a bug?

Many regards,

Sacha

On Nov 8, 4:02 pm, Victor Ruehle <rue...@votca.org> wrote:
> Hey,
>
> hmm, error message seems a bit misleading here. Did you put it in the
> sub tag <inverse> in non-bonded? so full path is
> cg.non-bonded.inverse.post_update_options.pressure.simple.scale
> and
> cg.non-bonded.inverse.p_target
>
> be aware the _, not - in p_target
>
> Best,
> Victor
>

> 2011/11/8 Sacha Mould <sacha...@gmail.com>:

[fri...@mpip-mainz.mpg.de]

Hi Sascha,

if I am not mistaken, I think you have to set the pressure correction
for each non-bonded interaction you are using. From your output it
seems to work for A-A, but fail for A-B and B-B interactions. Try to
set the other two as well. If it still doesent work, please share your
full settings.xml file with us. If what I wrote helps, it seems to be
indeed a bug as it should be possible to pressure correct selected
interactions.

Cheers
Sebastian

----------------------------------------------------------------
This message was sent using IMP, the Internet Messaging Program.

[Sacha Mould]

Hi Sebastian,

sure i can share my script. In this case i'm using only one type of
bonded interaction (B-B). All the beads are the same, with the same
mass. Here it goes the script:

<cg>
<non-bonded>
<name>B-B</name>
<type1>B</type1>
<type2>B</type2>
<min>0</min>
<max>1.5</max>
<step>0.001</step>
<inverse>
<target>B-B.dist.tgt</target>
<do_potential>0 1 0</do_potential>

<post_update>pressure</post_update>
<post_update_options>
<pressure>
<type>simple</type>
<do>0 0 1</do>
<simple>

<scale>0.37415295</scale>
</simple>
</pressure>
</post_update_options>
<post_update>smooth</post_update>
<post_update_options>
<smooth>
<iterations>2</iterations>
</smooth>
</post_update_options>
<post_update_options></post_update_options>
<post_add>convergence</post_add>
<post_add_options></post_add_options>
<p_target>1</p_target>
<particle_dens>3.2965079</particle_dens>
<gromacs>
<table>table_B_B.xvg</table>
</gromacs>
</inverse>
</non-bonded>
<inverse>
<kBT>3.55861028</kBT>
<program>gromacs</program>
<gromacs>
<equi_time>10</equi_time>
<table_bins>0.001</table_bins>
<pot_max>1000000</pot_max>
<table_end>2.5</table_end>
<temp_check>no</temp_check>
<cutoff_check>no</cutoff_check>
</gromacs>
<filelist>grompp.mdp topol.top table.xvg table_a1.xvg table_b1.xvg
index.ndx</filelist>
<iterations_max>500</iterations_max>
<convergence_check>default</convergence_check>
<convergence_check_options>
<limit>0.001</limit>
<name_glob>*.conv</name_glob>
</convergence_check_options>
<method>ibi</method>
<log_file>inverse.log</log_file>
<restart_file>restart_points.log</restart_file>
</inverse>
</cg>

Thanks a lot,

Sacha

[Victor Ruehle]

Hmm, looks alright to me. I vaguely remember there was a bug in
pressure correction which christoph fixed middle of october. How old
is your installation? An upgrade might help....

http://csg.votca.googlecode.com/hg-history/default/share/scripts/inverse/pressure_cor_simple.pl
is the newest one, you could compare with your votca installation in
<votca-path>/share/scripts/inverse/pressure_cor_simple.pl

Victor

2011/11/8 Sacha Mould <sach...@gmail.com>:

[Sacha Mould]

Hi all,

it seems that i figured it out. In my initial script i was calling two
post-updates, 'smooth' and 'pressure':

<post_update>pressure</post_update>
<post_update_options>
<pressure>
<type>simple</type>
<do>0 0 1</do>
<simple>
<scale>0.37415295</
scale>
</simple>
</pressure>
</post_update_options>
<post_update>smooth</post_update>
<post_update_options>
<smooth>
<iterations>2</iterations>
</smooth>
</post_update_options>

In this case, the simulation will run, but only the 'smooth' post-
update will perform and the 'pressure correction will be ignored. In
case i change the order and put the pressure correction after the
smooth, the simulation will through me the error that i posted on the
earlier message. So, i decided to put both of them between the same
<post-update-options> section, like this:

<post_update>smooth</post_update>
<post_update>pressure</post_update>

<post_update_options>
<smooth>
<iterations>2</iterations>
</smooth>

<pressure>
<type>wjk</type>
<do>1 0 0</do>
<wjk>
<scale>-0.355861028</scale>
</wjk>
</pressure>
</post_update_options>

In that case, the pressure correction will be performed without a
problem, but the smoothing fails. If i again change the order of them,
this time putting the pressure post-update first, smoothing will be
performed and pressure correction will fail. It seems that i can't
call those two post-updates, because votca will only accept one of
them, usually the one that is assigned at last.

Many regards,

Sacha

On Nov 8, 7:43 pm, Victor Ruehle <rue...@votca.org> wrote:
> Hmm, looks alright to me. I vaguely remember there was a bug in
> pressure correction which christoph fixed middle of october. How old
> is your installation? An upgrade might help....
>

> http://csg.votca.googlecode.com/hg-history/default/share/scripts/inve...

> is the newest one, you could compare with your votca installation in
> <votca-path>/share/scripts/inverse/pressure_cor_simple.pl
>
> Victor
>

> 2011/11/8 Sacha Mould <sacha...@gmail.com>:

> >> >> > For more options, visit...
>
> read more »

[Christoph Junghans]

Hi,

try to replace:

<post_update>smooth</post_update>
<post_update>pressure</post_update>

by
<post_update>smooth pressure</post_update>

Cheers,

Christoph

> For more options, visit this group at http://groups.google.com/group/votca?hl=en.
>
>

--
Christoph Junghans
Votca Core Developer

Web: http://www.votca.org

[Sacha Mould]

Hi Christoph,

it works!!!! Thanks so much!!!!

All the best,

Sacha

On Nov 9, 3:19 am, Christoph Junghans <jungh...@votca.org> wrote:
> Hi,
>
> try to replace:
>                         <post_update>smooth</post_update>
>                         <post_update>pressure</post_update>
> by
>                         <post_update>smooth pressure</post_update>
>
> Cheers,
>
> Christoph
>

> >> >> > Is there any possibility of...
>
> read more »

[Christoph Junghans]

And yes, this is a bug: <https://code.google.com/p/votca/issues/detail?id=121>

Christoph

[Victor Nazarychev]

Dear Votca users,

I have a simple question.  It is unclear for me how can I calculate the <particle_dens> for pressure correction. Could you, please, suggest some example, where how this value is calculated?  My model is consists of 1000 chains, each chain has 5 CG particles: 2 of type A and 3 of type B.  Could you help me, what <particle_dens> values should I use for non-bonded A-A, B-B, and A-B interactions?

Best regards,
Victor 

среда, 9 ноября 2011 г. в 22:26:32 UTC+4, Christoph Junghans:

[Christoph Junghans]

On Sat, Oct 29, 2022 at 10:14 Victor Nazarychev <nazar...@gmail.com> wrote:

Dear Votca users,

I have a simple question.  It is unclear for me how can I calculate the <particle_dens> for pressure correction. Could you, please, suggest some example, where how this value is calculated?  My model is consists of 1000 chains, each chain has 5 CG particles: 2 of type A and 3 of type B.  Could you help me, what <particle_dens> values should I use for non-bonded A-A, B-B, and A-B interactions?

it has been a long time , but if I remember correctly the wjk correction was only derived for a single component system. You would have to extend the calculation for multi-component system. I assume it would just map to the partial pressures.

Christoph

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[Victor Nazarychev]

Dear Christoph, 

Thank you very much for your help. I tried to find how to calcualte partial pressures, but did not find any information about it. Maybe you could suggest how to calculate partial pressures with Gromacs?  

Best regards, 

Victor 

сб, 29 окт. 2022 г. в 22:17, Christoph Junghans <jung...@votca.org>:

To view this discussion on the web visit https://groups.google.com/d/msgid/votca/CAHG27e6vvXvA5se0FmRiDhsJfMVgkkw%2BLRPQu8fQMtxO6yo8dQ%40mail.gmail.com.

[Christoph Junghans]

On Sun, Oct 30, 2022 at 10:21 AM Victor Nazarychev <nazar...@gmail.com> wrote:
>
> Dear Christoph,
>
> Thank you very much for your help. I tried to find how to calcualte partial pressures, but did not find any information about it. Maybe you could suggest how to calculate partial pressures with Gromacs?

If I remember correctly, gromacs doesn't support partial pressures,
but lammps does. Might be more a question for the gromacs mailing list
though.

We had modified gromacs at some point, but this change never made it
upstream. There is a local pressure version in Sikandar's gromacs
fork:
https://github.com/symashayak/gromacs/tree/release-4-6-1-localpressure_slab
But I am not sure that was the right version.

Christoph

> To view this discussion on the web visit https://groups.google.com/d/msgid/votca/CALpHq2e-HrmYpd1B_9gWCG-zmxVssKM-nPY7Tsf%3DU1fOB7XezA%40mail.gmail.com.

[Victor Nazarychev]

Dear Cristoph, 

Thank you very much. 

Victor

воскресенье, 30 октября 2022 г. в 20:26:38 UTC+3, Christoph Junghans: